[gmx-users] Help in parametrisation

[Justin A. Lemkul]

onetwo wrote:
> Thanks Justin for the help,
> 
> I have Manganese in my protein with other two ligands at the active site.
> I am using GROMOS96 43a1 force field.
> 
> Mangnese may have topology similar to Magnesium 2+, What I found is that 

Assuming a transition metal "may" be similar to another species is probably a 
pretty poor assumption.  Prepare for lots of criticism if you proceed with that 
thought.

> I need to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I 
> calculate the nonbond_params for ffG43a1nb.itp.
> 

Refer to the other GROMOS papers for how they derive parameters for small 
molecules.  I've never seen a demonstration of transition metal parameterization 
under these force fields, though.  Perhaps you should be using an AMBER force 
field that contains Mn2+.  Any particular reason you think you need GROMOS?

> For both the other two ligands which contains phosphate and enol groups, 
> I was able to create topology using PRODRG server.

Please pay careful attention to the second paragraph here:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips

-Justin

> 
> Regards
> 
> onetwo wrote:
>  > Hello All,
>  >
>  > I am new in this field, and I want to do simulation study on one of 
> the protein conatining a metal ion and study its ability to form 
> co-oridnation bond with other ligand, which is not defined in GROMOS 
> force field which I have tried. If this choice of force field is correct 
> for such type of study ?
>  >
>  > I have read Gromacs Manual Chapter 5, also I am following this 
> gromacs mailing list for quite some time to get a help on how to include 
> a new metal ion or a new ligand in their simulation and they have been 
> refered to refer to the 
> http://www.gromacs.org/Documentation/How-tos/Parameterization,
>  >
>  > but in this its not mentioned that how to actually do parameterization
>  >
>  > neither in manual it has been told on how to generate it ( due 
> apologies,,I know, I may be wrong )
>  >
> 
> The manual will not cover every possible topic. Parameterization is 
> described in the primary literature for the force field you wish you 
> use. "GROMOS" is not very specific - there are numerous parameter sets 
> within this class of force field.
> 
>  > and it is more difficult for a person like me who doesnt have much 
> knowledge in this field, so if someone can please help me guiding how to 
> do parameterisation, I know this is not a trivial task, but still help 
> in this regard may help many other fellow users besides me.
> 
> Aside from telling you to read all the literature you can, there's not 
> much more help anyone can do to help you. You haven't described very 
> well what your system is. What kind of functional groups are in your 
> ligand? If the functional groups are shared with existing parameters, 
> then you'll have a rather easy time constructing a topology. What type 
> of metal ion is it? If you're dealing with a transition metal, using a 
> standard MM force field may not work very well. Note the "Exotic 
> Species" heading on the page you quoted above.
> 
> -Justin
> 
>  > Thanks in advance
>  >
>  >
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================